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Day 4: Read QC and Intro to Mapping

Welcome to Day 4 of the Short-Read Sequencing Analysis Workshop. After Day 4 you should have a basic understanding of how to use FastQC to evaluate the quality of your short-read data and how to trim your reads using Trimmomatic. We will also be reviewing barcoding/indexing and some of the considerations to using barcodes for multiplex sequencing.

Day 4 Videos

Video1: Barcoding This video will go over many of the design considerations for barcoding/indexing, as well as the demultiplexing process Slides for Video1

Video2: Post-sequencing quality evaluation This video will explain the fastq file format, review some of the sources of library read quality problems and introduce you to the FastQC program. In addition it will explain how to troubleshoot various problems using the FastQC program output. Slides for Video2

Video3: Running FastQC This video will walk through an example of read quality evaluation with FastQC

Video4: Running Trimmomatic This video will introduce you to the Trimmomatic program that can be used to trim reads for adapter contamination or low quality bases. Slides for Video4 

Day 4 files

Day4 In-class slides (available at the start of class)

Day4 Homework (available at the start of class)

Day4 Homework solutions (available at the start of class)

Additional resources

FastQC website 

Another FastQC video

FastQC manual (pdf file)

Trimmomatic website

Trimmomatic manual (pdf file)

Trimmomatic paper (pdf file)


Videos and files from 2014 

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